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論文リスト

doi title author source_title year
4987 10.1016/j.ajog.2018.10.018 Does The Human Placenta Delivered At Term Have A Microbiota? Results Of Cultivation, Quantitative Real-Time Pcr, 16S Rrna Gene Sequencing, And Metagenomics Theis, Kevin R.; Romero, Roberto, 0000-0002-4448-5121; Winters, Andrew D.; Greenberg, Jonathan M.; Gomez-Lopez, Nardhy; Alhousseini, Ali; Bieda, Janine; Maymon, Eli; Pacora, Percy; Fettweis, Jennifer M.; Buck, Gregory A.; Jefferson, Kimberly K., 0000-0003-1052-1988; Strauss, Jerome F.; Erez, Offer, 0000-0002-0680-7652; Hassan, Sonia S. American Journal Of Obstetrics And Gynecology 2019
7069 10.1016/j.cej.2018.09.218 Removal Of Antibiotic Resistance Genes And Control Of Horizontal Transfer Risk By Uv, Chlorination And Uv/Chlorination Treatments Of Drinking Water Zhang, Tianyang, 0000-0002-9522-5354; Hu, Yaru; Jiang, Lei; Yao, Shijie; Lin, Kuangfei; Zhou, Yanbo, 0000-0003-1756-7073; Cui, Changzheng Chemical Engineering Journal 2019
7539 10.1016/j.cell.2018.10.029 Us Immigration Westernizes The Human Gut Microbiome Vangay, Pajau; Johnson, Abigail J.; Ward, Tonya L.; Al-Ghalith, Gabriel A.; Shields-Cutler, Robin R.; Hillmann, Benjamin M.; Lucas, Sarah K.; Beura, Lalit K.; Thompson, Emily A.; Till, Lisa M.; Batres, Rodolfo; Paw, Bwei; Pergament, Shannon L.; Saenyakul, Pimpanitta; Xiong, Mary; Kim, Austin D.; Kim, Grant; Masopust, David; Martens, Eric C.; Angkurawaranon, Chaisiri; Mcgready, Rose; Kashyap, Purna C.; Culhane-Pera, Kathleen A.; Knights, Dan Cell 2018
7585 10.1016/j.cell.2019.01.001 Extensive Unexplored Human Microbiome Diversity Revealed By Over 150,000 Genomes From Metagenomes Spanning Age, Geography, And Lifestyle Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena; Zolfo, Moreno; Karcher, Nicolai; Armanini, Federica; Beghini, Francesco; Manghi, Paolo; Tett, Adrian; Ghensi, Paolo; Collado, Maria Carmen; Rice, Benjamin L.; Dulong, Casey; Morgan, Xochitl C.; Golden, Christopher D.; Quince, Christopher; Huttenhower, Curtis; Segata, Nicola, 0000-0002-1583-5794 Cell 2019
7704 10.1016/j.cell.2019.07.010 Benchmarking Metagenomics Tools For Taxonomic Classification Ye, Simon H.; Siddle, Katherine J.; Park, Daniel J.; Sabeti, Pardis C. Cell 2019
8416 10.1016/j.chom.2018.06.005 Mother-To-Infant Microbial Transmission From Different Body Sites Shapes The Developing Infant Gut Microbiome Ferretti, Pamela; Pasolli, Edoardo; Tett, Adrian; Asnicar, Francesco; Gorfer, Valentina; Fedi, Sabina; Armanini, Federica; Truong, Duy Tin; Manara, Serena; Zolfo, Moreno; Beghini, Francesco; Bertorelli, Roberto; De Sanctis, Veronica; Bariletti, Ilaria; Canto, Rosarita; Clementi, Rosanna; Cologna, Marina; Crifo, Tiziana; Cusumano, Giuseppina; Gottardi, Stefania; Innamorati, Claudia; Mase, Caterina; Postai, Daniela; Savoi, Daniela; Duranti, Sabrina; Lugli, Gabriele Andrea; Mancabelli, Leonardo; Turroni, Francesca; Ferrario, Chiara; Milani, Christian; Mangifesta, Marta; Anzalone, Rosaria; Viappiani, Alice; Yassour, Moran; Vlamakis, Hera; Xavier, Ramnik; Collado, Carmen Maria; Koren, Omry; Tateo, Saverio; Soffiati, Massimo; Pedrotti, Anna; Ventura, Marco; Huttenhower, Curtis; Bork, Peer; Segata, Nicola, 0000-0002-1583-5794 Cell Host & Microbe 2018
8428 10.1016/j.chom.2019.01.004 Distinct Genetic And Functional Traits Of Human Intestinal Prevotella Copri Strains Are Associated With Different Habitual Diets De Filippis, Francesca; Pasolli, Edoardo; Tett, Adrian; Tarallo, Sonia; Naccarati, Alessio; De Angelis, Maria; Neviani, Erasmo; Cocolin, Luca; Gobbetti, Marco; Segata, Nicola; Ercolini, Danilo Cell Host & Microbe 2019
8432 10.1016/j.chom.2019.01.011 Composition And Variation Of The Human Milk Microbiota Are Influenced By Maternal And Early-Life Factors Moossavi, Shirin, 0000-0002-8329-9970; Sepehri, Shadi; Robertson, Bianca; Bode, Lars; Goruk, Sue; Field, Catherine J.; Lix, Lisa M.; De Souza, Russell J.; Becker, Allan B.; Mandhane, Piushkumar J.; Turvey, Stuart E.; Subbarao, Padmaja; Moraes, Theo J.; Lefebvre, Diana L.; Sears, Malcolm R.; Khafipour, Ehsan; Azad, Meghan B. Cell Host & Microbe 2019
8438 10.1016/j.chom.2019.03.007 Adaptive Evolution Within Gut Microbiomes Of Healthy People Zhao, Shijie; Lieberman, Tami D.; Poyet, Mathilde; Kauffman, Kathryn M.; Gibbons, Sean M.; Groussin, Mathieu; Xavier, Ramnik J.; Alm, Eric J. Cell Host & Microbe 2019
8447 10.1016/j.chom.2019.08.018 The Prevotella Copri Complex Comprises Four Distinct Clades Underrepresented In Westernized Populations Tett, Adrian; Huang, Kun D.; Asnicar, Francesco; Fehlner-Peach, Hannah; Pasolli, Edoardo; Karcher, Nicolai; Armanini, Federica; Manghi, Paolo; Bonham, Kevin; Zolfo, Moreno; De Filippis, Francesca; Magnabosco, Cara; Bonneau, Richard; Lusingu, John; Amuasi, John; Reinhard, Karl; Rattei, Thomas; Boulund, Fredrik; Engstrand, Lars; Zink, Albert; Collado, Maria Carmen; Littman, Dan R.; Eibach, Daniel; Ercolini, Danilo; Rota-Stabelli, Omar; Huttenhower, Curtis; Maixner, Frank; Segata, Nicola Cell Host & Microbe 2019
10146 10.1016/j.envint.2018.03.044 Antibiotic Resistance In Wastewater Treatment Plants: Tackling The Black Box Manaia, Celia M., 0000-0002-3674-1789; Rocha, Jaqueline; Scaccia, Nazareno, 0000-0003-3294-3815; Marano, Roberto, 0000-0001-7805-6360; Radu, Elena; Biancullo, Francesco, 0000-0002-4363-9141; Cerqueira, Francisco, 0000-0003-4812-0880; Fortunato, Gianuario; Iakovides, Iakovos C.; Zammit, Ian, 0000-0002-9768-6592; Kampouris, Ioannis; Vaz-Moreira, Ivone, 0000-0001-8912-9836; Nunes, Olga C., 0000-0003-4742-2537 Environment International 2018
10149 10.1016/j.envint.2018.04.041 Critical Knowledge Gaps And Research Needs Related To The Environmental Dimensions Of Antibiotic Resistance Larsson, D.G. Joakim; Andremont, Antoine; Bengtsson-Palme, Johan, 0000-0002-6528-3158; Brandt, Kristian Koefoed, 0000-0001-7886-9708; De Roda Husman, Ana Maria; Fagerstedt, Patriq, 0000-0002-6639-3412; Fick, Jerker, 0000-0002-3949-7371; Flach, Carl-Fredrik; Gaze, William H.; Kuroda, Makoto, 0000-0002-0487-4405; Kvint, Kristian; Laxminarayan, Ramanan, 0000-0002-1390-9016; Manaia, Celia M., 0000-0002-3674-1789; Nielsen, Kaare Magne; Plant, Laura; Ploy, Marie-Cecile; Segovia, Carlos; Simonet, Pascal; Smalla, Kornelia; Snape, Jason; Topp, Edward; Van Hengel, Arjon J.; Verner-Jeffreys, David W.; Virta, Marko P.J.; Wellington, Elizabeth M.; Wernersson, Ann-Sofie Environment International 2018
10177 10.1016/j.envint.2019.01.034 Understanding Drivers Of Antibiotic Resistance Genes In High Arctic Soil Ecosystems Mccann, Clare M.; Christgen, Beate, 0000-0002-5662-8847; Roberts, Jennifer A.; Su, Jian-Qiang; Arnold, Kathryn E.; Gray, Neil D.; Zhu, Yong-Guan; Graham, David W. Environment International 2019
10201 10.1016/j.envint.2019.05.036 Metagenomic And Metatranscriptomic Analyses Reveal Activity And Hosts Of Antibiotic Resistance Genes In Activated Sludge Liu, Zongbao; Klumper, Uli; Liu, Yang; Yang, Yuchun; Wei, Qiaoyan; Lin, Jih-Gaw; Gu, Ji-Dong; Li, Meng Environment International 2019
10205 10.1016/j.envint.2019.104912 Transfer Of Antibiotic Resistance From Manure-Amended Soils To Vegetable Microbiomes Zhang, Yu-Jing; Hu, Hang-Wei; Chen, Qing-Lin; Singh, Brajesh K.; Yan, Hui; Chen, Deli; He, Ji-Zheng Environment International 2019
10329 10.1016/j.envpol.2019.112996 A Review On Removing Antibiotics And Antibiotic Resistance Genes From Wastewater By Constructed Wetlands: Performance And Microbial Response Liu, Xiaohui; Guo, Xiaochun; Liu, Ying; Lu, Shaoyong; Xi, Beidou; Zhang, Jian; Wang, Zhi; Bi, Bin Environmental Pollution 2019
13076 10.1016/j.jenvman.2019.05.090 Insights On The Current Status Of Occurrence And Removal Of Antibiotics In Wastewater By Advanced Oxidation Processes Anjali, R.; Shanthakumar, S. Journal Of Environmental Management 2019
16847 10.1016/j.scitotenv.2019.03.162 Antibiotic Resistance In Drinking Water Systems: Occurrence, Removal, And Human Health Risks Sanganyado, Edmond, 0000-0001-6244-3059; Gwenzi, Willis, 0000-0003-3149-1052 Science Of The Total Environment 2019
16885 10.1016/j.scitotenv.2019.05.315 Antibiotic Microbial Resistance (Amr) Removal Efficiencies By Conventional And Advanced Wastewater Treatment Processes: A Review Hiller, C.X.; Hubner, U.; Fajnorova, S.; Schwartz, T.; Drewes, J.E., 0000-0003-2520-7596 Science Of The Total Environment 2019
16914 10.1016/j.scitotenv.2019.134023 Antibiotic Resistance Genes Identified In Wastewater Treatment Plant Systems <U+2013> A Review Pazda, Magdalena; Kumirska, Jolanta, 0000-0003-1211-1114; Stepnowski, Piotr; Mulkiewicz, Ewa, 0000-0001-6144-1190 Science Of The Total Environment 2019
17308 10.1016/j.soilbio.2018.08.018 Antibiotic Resistance Genes And Associated Bacterial Communities In Agricultural Soils Amended With Different Sources Of Animal Manures Han, Xue-Mei; Hu, Hang-Wei; Chen, Qing-Lin; Yang, Li-Yuan; Li, He-Lian; Zhu, Yong-Guan; Li, Xiang-Zhen; Ma, Yi-Bing Soil Biology And Biochemistry 2018
17707 10.1016/j.tim.2018.06.007 Evolution Of Plasmid-Mediated Antibiotic Resistance In The Clinical Context San Millan, Alvaro Trends In Microbiology 2018
17709 10.1016/j.tim.2018.09.008 The Human Microbiome And Child Growth <U+2013> First 1000 Days And Beyond Robertson, Ruairi C., 0000-0002-3719-2056; Manges, Amee R.; Finlay, B. Brett; Prendergast, Andrew J. Trends In Microbiology 2019
17710 10.1016/j.tim.2018.11.003 Contamination In Low Microbial Biomass Microbiome Studies: Issues And Recommendations Eisenhofer, Raphael, 0000-0002-3843-0749; Minich, Jeremiah J.; Marotz, Clarisse; Cooper, Alan; Knight, Rob; Weyrich, Laura S. Trends In Microbiology 2019
17715 10.1016/j.tim.2019.08.001 The Gut Microbiota In The First Decade Of Life Derrien, Muriel; Alvarez, Anne-Sophie; De Vos, Willem M. Trends In Microbiology 2019
17826 10.1016/j.tplants.2019.02.010 Antibiotic Resistomes In Plant Microbiomes Chen, Qing-Lin; Cui, Hui-Ling; Su, Jian-Qiang; Penuelas, Josep; Zhu, Yong-Guan Trends In Plant Science 2019
18144 10.1016/j.watres.2018.08.048 Comparison Of The Uv/Chlorine And Uv/H2O2 Processes In The Degradation Of Ppcps In Simulated Drinking Water And Wastewater: Kinetics, Radical Mechanism And Energy Requirements Guo, Kaiheng, 0000-0002-8168-4605; Wu, Zihao; Yan, Shuwen; Yao, Bo; Song, Weihua, 0000-0001-7633-7919; Hua, Zhechao; Zhang, Xuewen; Kong, Xiujuan; Li, Xuchun; Fang, Jingyun Water Research 2018
18158 10.1016/j.watres.2018.11.041 Ppcp Degradation And Dbp Formation In The Solar/Free Chlorine System: Effects Of Ph And Dissolved Oxygen Hua, Zhechao; Guo, Kaiheng, 0000-0002-8168-4605; Kong, Xiujuan; Lin, Suiki; Wu, Zihao; Wang, Liping; Huang, Huang; Fang, Jingyun Water Research 2019
18206 10.1016/j.watres.2019.06.039 Antibiotic Resistance Genes In Treated Wastewater And In The Receiving Water Bodies: A Pan-European Survey Of Urban Settings Cacace, Damiano, 0000-0003-1725-1044; Fatta-Kassinos, Despo; Manaia, Celia M., 0000-0002-3674-1789; Cytryn, Eddie, 0000-0001-7805-6360; Kreuzinger, Norbert; Rizzo, Luigi, 0000-0003-1449-9116; Karaolia, Popi; Schwartz, Thomas; Alexander, Johannes; Merlin, Christophe; Garelick, Hemda; Schmitt, Heike; De Vries, Daisy; Schwermer, Carsten U.; Meric, Sureyya; Ozkal, Can Burak, 0000-0001-9576-2582; Pons, Marie-Noelle; Kneis, David; Berendonk, Thomas U. Water Research 2019
20176 10.1021/acs.est.8b04393 Degradation And Deactivation Of Bacterial Antibiotic Resistance Genes During Exposure To Free Chlorine, Monochloramine, Chlorine Dioxide, Ozone, Ultraviolet Light, And Hydroxyl Radical He, Huan; Zhou, Peiran; Shimabuku, Kyle K., 0000-0001-8497-5945; Fang, Xuzhi; Li, Shu; Lee, Yunho, 0000-0001-5923-4897; Dodd, Michael C., 0000-0001-7544-1642 Environmental Science & Technology 2019
20229 10.1021/acs.est.9b02462 Rate Constants And Mechanisms Of The Reactions Of Cl<U+2022> And Cl2<U+2022><U+2013> With Trace Organic Contaminants Lei, Yu; Cheng, Shuangshuang; Luo, Na; Yang, Xin, 0000-0001-9860-423X; An, Taicheng, 0000-0001-6918-8070 Environmental Science & Technology 2019
22106 10.1038/nbt.4229 A Standardized Bacterial Taxonomy Based On Genome Phylogeny Substantially Revises The Tree Of Life Parks, Donovan H; Chuvochina, Maria; Waite, David W; Rinke, Christian, 0000-0003-4632-1187; Skarshewski, Adam; Chaumeil, Pierre-Alain; Hugenholtz, Philip, 0000-0001-5386-7925 Nature Biotechnology 2018
22307 10.1038/s41396-018-0277-8 Wastewater Treatment Plant Resistomes Are Shaped By Bacterial Composition, Genetic Exchange, And Upregulated Expression In The Effluent Microbiomes Ju, Feng, 0000-0003-4137-5928; Beck, Karin; Yin, Xiaole; Maccagnan, Andreas; Mcardell, Christa S., 0000-0002-5251-7541; Singer, Heinz P., 0000-0002-8542-3699; Johnson, David R., 0000-0002-6728-8462; Zhang, Tong; Burgmann, Helmut, 0000-0002-5651-5906 The Isme Journal 2018
22318 10.1038/s41396-019-0446-4 Linking The Resistome And Plasmidome To The Microbiome Stalder, Thibault; Press, Maximilian O.; Sullivan, Shawn; Liachko, Ivan; Top, Eva M., 0000-0002-6380-8782 The Isme Journal 2019
22324 10.1038/s41396-019-0553-2 Breast Milk-Derived Human Milk Oligosaccharides Promote Bifidobacterium Interactions Within A Single Ecosystem Lawson, Melissa A. E.; O’Neill, Ian J.; Kujawska, Magdalena, 0000-0002-8842-3512; Gowrinadh Javvadi, Sree; Wijeyesekera, Anisha, 0000-0001-6151-5065; Flegg, Zak; Chalklen, Lisa, 0000-0002-6162-9940; Hall, Lindsay J., 0000-0001-8938-5709 The Isme Journal 2019
22327 10.1038/s41396-020-0590-x Anaerobic Methane Oxidation Coupled To Manganese Reduction By Members Of The Methanoperedenaceae Leu, Andy O.; Cai, Chen, 0000-0002-0167-1397; Mcilroy, Simon J., 0000-0003-3749-8730; Southam, Gordon; Orphan, Victoria J.; Yuan, Zhiguo, 0000-0002-7566-1482; Hu, Shihu; Tyson, Gene W., 0000-0001-8559-9427 The Isme Journal 2020
22610 10.1038/s41467-018-06393-w Maternal Gut And Breast Milk Microbiota Affect Infant Gut Antibiotic Resistome And Mobile Genetic Elements Parnanen, Katariina; Karkman, Antti; Hultman, Jenni, 0000-0002-3431-1785; Lyra, Christina; Bengtsson-Palme, Johan, 0000-0002-6528-3158; Larsson, D. G. Joakim, 0000-0002-5496-0328; Rautava, Samuli; Isolauri, Erika; Salminen, Seppo; Kumar, Himanshu; Satokari, Reetta; Virta, Marko, 0000-0001-5981-7566 Nature Communications 2018
22614 10.1038/s41467-018-06473-x Meta-Analysis Of Effects Of Exclusive Breastfeeding On Infant Gut Microbiota Across Populations Ho, Nhan T.; Li, Fan; Lee-Sarwar, Kathleen A.; Tun, Hein M.; Brown, Bryan P.; Pannaraj, Pia S.; Bender, Jeffrey M.; Azad, Meghan B.; Thompson, Amanda L.; Weiss, Scott T.; Azcarate-Peril, M. Andrea; Litonjua, Augusto A.; Kozyrskyj, Anita L.; Jaspan, Heather B.; Aldrovandi, Grace M.; Kuhn, Louise Nature Communications 2018
22687 10.1038/s41467-018-07418-0 Expansive Microbial Metabolic Versatility And Biodiversity In Dynamic Guaymas Basin Hydrothermal Sediments Dombrowski, Nina, 0000-0003-1917-2577; Teske, Andreas P.; Baker, Brett J. Nature Communications 2018
22714 10.1038/s41467-018-07631-x Birth Mode Is Associated With Earliest Strain-Conferred Gut Microbiome Functions And Immunostimulatory Potential Wampach, Linda; Heintz-Buschart, Anna, 0000-0002-9780-1933; Fritz, Joelle V.; Ramiro-Garcia, Javier; Habier, Janine; Herold, Malte; Narayanasamy, Shaman; Kaysen, Anne; Hogan, Angela H.; Bindl, Lutz, 0000-0003-1764-434X; Bottu, Jean; Halder, Rashi, 0000-0002-1402-1254; Sjoqvist, Conny; May, Patrick, 0000-0001-8698-3770; Andersson, Anders F., 0000-0002-3627-6899; De Beaufort, Carine; Wilmes, Paul Nature Communications 2018
22717 10.1038/s41467-018-07641-9 High Throughput Ani Analysis Of 90K Prokaryotic Genomes Reveals Clear Species Boundaries Jain, Chirag; Rodriguez-R, Luis M., 0000-0001-7603-3093; Phillippy, Adam M.; Konstantinidis, Konstantinos T.; Aluru, Srinivas Nature Communications 2018
22771 10.1038/s41467-018-07992-3 Fecal Pollution Can Explain Antibiotic Resistance Gene Abundances In Anthropogenically Impacted Environments Karkman, Antti, 0000-0003-0983-3319; Parnanen, Katariina; Larsson, D. G. Joakim, 0000-0002-5496-0328 Nature Communications 2019
22899 10.1038/s41467-019-08844-4 Microbial Abundance, Activity And Population Genomic Profiling With Motus2 Milanese, Alessio, 0000-0002-7050-2239; Mende, Daniel R, 0000-0001-6831-4557; Paoli, Lucas; Salazar, Guillem; Ruscheweyh, Hans-Joachim; Cuenca, Miguelangel, 0000-0003-3435-9102; Hingamp, Pascal; Alves, Renato, 0000-0002-7212-0234; Costea, Paul I, 0000-0003-1645-3947; Coelho, Luis Pedro, 0000-0002-9280-7885; Schmidt, Thomas S. B., 0000-0001-8587-4177; Almeida, Alexandre, 0000-0001-8803-0893; Mitchell, Alex L; Finn, Robert D., 0000-0001-8626-2148; Huerta-Cepas, Jaime; Bork, Peer, 0000-0002-2627-833X; Zeller, Georg, 0000-0003-1429-7485; Sunagawa, Shinichi, 0000-0003-3065-0314 Nature Communications 2019
22900 10.1038/s41467-019-08853-3 Global Monitoring Of Antimicrobial Resistance Based On Metagenomics Analyses Of Urban Sewage Hendriksen, Rene S.; Munk, Patrick, 0000-0001-8813-4019; Njage, Patrick; Van Bunnik, Bram, 0000-0003-2177-7073; Mcnally, Luke; Lukjancenko, Oksana; Roder, Timo; Nieuwenhuijse, David; Pedersen, Susanne Karlsmose; Kjeldgaard, Jette; Kaas, Rolf S.; Clausen, Philip Thomas Lanken Conradsen; Vogt, Josef Korbinian; Leekitcharoenphon, Pimlapas; Van De Schans, Milou G. M.; Zuidema, Tina; De Roda Husman, Ana Maria; Rasmussen, Simon, 0000-0001-6323-9041; Petersen, Bent; Amid, Clara; Cochrane, Guy; Sicheritz-Ponten, Thomas; Schmitt, Heike; Alvarez, Jorge Raul Matheu; Aidara-Kane, Awa; Pamp, Sunje J.; Lund, Ole; Hald, Tine; Woolhouse, Mark; Koopmans, Marion P.; Vigre, Hakan; Petersen, Thomas Nordahl; Aarestrup, Frank M., 0000-0002-7116-2723 Nature Communications 2019
22967 10.1038/s41467-019-09252-4 Perinatal Factors Affect The Gut Microbiota Up To Four Years After Birth Fouhy, Fiona, 0000-0002-8285-7694; Watkins, Claire; Hill, Cian J.; O’Shea, Carol-Anne; Nagle, Brid; Dempsey, Eugene M.; O’Toole, Paul W.; Ross, R. Paul; Ryan, C. Anthony; Stanton, Catherine Nature Communications 2019
22987 10.1038/s41467-019-09364-x Asgard Archaea Capable Of Anaerobic Hydrocarbon Cycling Seitz, Kiley W.; Dombrowski, Nina, 0000-0003-1917-2577; Eme, Laura, 0000-0002-0510-8868; Spang, Anja; Lombard, Jonathan; Sieber, Jessica R.; Teske, Andreas P.; Ettema, Thijs J. G., 0000-0002-6898-6377; Baker, Brett J. Nature Communications 2019
23141 10.1038/s41467-019-10656-5 Establishing Microbial Composition Measurement Standards With Reference Frames Morton, James T.; Marotz, Clarisse, 0000-0002-1520-8854; Washburne, Alex; Silverman, Justin; Zaramela, Livia S., 0000-0002-1065-3799; Edlund, Anna; Zengler, Karsten, 0000-0002-8062-3296; Knight, Rob, 0000-0002-0975-9019 Nature Communications 2019
23358 10.1038/s41467-019-13443-4 Phylogenomics Of 10,575 Genomes Reveals Evolutionary Proximity Between Domains Bacteria And Archaea Zhu, Qiyun, 0000-0002-3568-6271; Mai, Uyen; Pfeiffer, Wayne; Janssen, Stefan, 0000-0003-0955-0589; Asnicar, Francesco, 0000-0003-3732-1468; Sanders, Jon G., 0000-0001-6077-4014; Belda-Ferre, Pedro, 0000-0001-6532-1161; Al-Ghalith, Gabriel A., 0000-0002-6953-6319; Kopylova, Evguenia; Mcdonald, Daniel; Kosciolek, Tomasz, 0000-0002-9915-7387; Yin, John B.; Huang, Shi; Salam, Nimaichand; Jiao, Jian-Yu; Wu, Zijun; Xu, Zhenjiang Z.; Cantrell, Kalen; Yang, Yimeng, 0000-0003-4819-1005; Sayyari, Erfan; Rabiee, Maryam; Morton, James T.; Podell, Sheila, 0000-0001-7073-5190; Knights, Dan; Li, Wen-Jun, 0000-0002-1233-736X; Huttenhower, Curtis, 0000-0002-1110-0096; Segata, Nicola, 0000-0002-1583-5794; Smarr, Larry; Mirarab, Siavash, 0000-0001-5410-1518; Knight, Rob, 0000-0002-0975-9019 Nature Communications 2019
23497 10.1038/s41467-020-16366-7 Precise Phylogenetic Analysis Of Microbial Isolates And Genomes From Metagenomes Using Phylophlan 3.0 Asnicar, Francesco, 0000-0003-3732-1468; Thomas, Andrew Maltez, 0000-0001-5789-3354; Beghini, Francesco, 0000-0002-8105-9607; Mengoni, Claudia; Manara, Serena, 0000-0001-6371-528X; Manghi, Paolo; Zhu, Qiyun; Bolzan, Mattia, 0000-0001-8539-9468; Cumbo, Fabio, 0000-0003-2920-5838; May, Uyen; Sanders, Jon G., 0000-0001-6077-4014; Zolfo, Moreno, 0000-0001-6661-4046; Kopylova, Evguenia; Pasolli, Edoardo; Knight, Rob, 0000-0002-0975-9019; Mirarab, Siavash, 0000-0001-5410-1518; Huttenhower, Curtis, 0000-0002-1110-0096; Segata, Nicola, 0000-0002-1583-5794 Nature Communications 2020
23951 10.1038/s41559-019-1040-x Phylogenomics Provides Robust Support For A Two-Domains Tree Of Life Williams, Tom A., 0000-0003-1072-0223; Cox, Cymon J., 0000-0002-4927-979X; Foster, Peter G.; Szoll<U+0151>si, Gergely J.; Embley, T. Martin Nature Ecology & Evolution 2019
24332 10.1038/s41564-018-0171-1 Recovery Of Genomes From Metagenomes Via A Dereplication, Aggregation And Scoring Strategy Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison; Thomas, Brian C.; Hess, Matthias; Tringe, Susannah G., 0000-0001-6479-8427; Banfield, Jillian F., 0000-0001-8203-8771 Nature Microbiology 2018
24335 10.1038/s41564-018-0202-y Recognizing The Reagent Microbiome De Goffau, Marcus C.; Lager, Susanne; Salter, Susannah J.; Wagner, Josef; Kronbichler, Andreas; Charnock-Jones, D. Stephen; Peacock, Sharon J.; Smith, Gordon C. S.; Parkhill, Julian Nature Microbiology 2018
24344 10.1038/s41564-018-0321-5 Genomic Variation And Strain-Specific Functional Adaptation In The Human Gut Microbiome During Early Life Vatanen, Tommi, 0000-0003-0949-1291; Plichta, Damian R.; Somani, Juhi; Munch, Philipp C.; Arthur, Timothy D.; Hall, Andrew Brantley; Rudolf, Sabine; Oakeley, Edward J.; Ke, Xiaobo; Young, Rachel A.; Haiser, Henry J.; Kolde, Raivo; Yassour, Moran; Luopajarvi, Kristiina; Siljander, Heli; Virtanen, Suvi M.; Ilonen, Jorma; Uibo, Raivo; Tillmann, Vallo; Mokurov, Sergei; Dorshakova, Natalya; Porter, Jeffrey A.; Mchardy, Alice C., 0000-0003-2370-3430; Lahdesmaki, Harri; Vlamakis, Hera; Huttenhower, Curtis, 0000-0002-1110-0096; Knip, Mikael, 0000-0003-0474-0033; Xavier, Ramnik J., 0000-0002-5630-5167 Nature Microbiology 2018
24355 10.1038/s41564-019-0363-3 Wide Diversity Of Methane And Short-Chain Alkane Metabolisms In Uncultured Archaea Borrel, Guillaume, 0000-0003-4893-8180; Adam, Panagiotis S.; Mckay, Luke J., 0000-0003-2942-1821; Chen, Lin-Xing; Sierra-Garcia, Isabel Natalia; Sieber, Christian M. K.; Letourneur, Quentin; Ghozlane, Amine; Andersen, Gary L.; Li, Wen-Jun, 0000-0002-1233-736X; Hallam, Steven J., 0000-0002-4889-6876; Muyzer, Gerard, 0000-0002-2422-0732; De Oliveira, Valeria Maia; Inskeep, William P., 0000-0002-5203-817X; Banfield, Jillian F., 0000-0001-8203-8771; Gribaldo, Simonetta, 0000-0002-7662-021X Nature Microbiology 2019
24360 10.1038/s41564-019-0406-9 Proposal Of The Reverse Flow Model For The Origin Of The Eukaryotic Cell Based On Comparative Analyses Of Asgard Archaeal Metabolism Spang, Anja, 0000-0002-6518-8556; Stairs, Courtney W., 0000-0001-6650-0970; Dombrowski, Nina; Eme, Laura, 0000-0002-0510-8868; Lombard, Jonathan; Caceres, Eva F.; Greening, Chris, 0000-0001-7616-0594; Baker, Brett J.; Ettema, Thijs J. G., 0000-0002-6898-6377 Nature Microbiology 2019
24362 10.1038/s41564-019-0409-6 Transmission Of Human-Associated Microbiota Along Family And Social Networks Brito, Ilana L.; Gurry, Thomas; Zhao, Shijie; Huang, Katherine; Young, Sarah K.; Shea, Terrence P.; Naisilisili, Waisea; Jenkins, Aaron P.; Jupiter, Stacy D.; Gevers, Dirk; Alm, Eric J., 0000-0001-8294-9364 Nature Microbiology 2019
24364 10.1038/s41564-019-0426-5 Global Diversity And Biogeography Of Bacterial Communities In Wastewater Treatment Plants Wu, Linwei; Ning, Daliang; Zhang, Bing; Li, Yong; Zhang, Ping; Shan, Xiaoyu; Zhang, Qiuting; Brown, Mathew Robert; Li, Zhenxin; Van Nostrand, Joy D., 0000-0001-9548-6450; Ling, Fangqiong; Xiao, Naijia; Zhang, Ya; Vierheilig, Julia, 0000-0002-9764-7534; Wells, George F.; Yang, Yunfeng, 0000-0001-8274-6196; Deng, Ye, 0000-0002-7584-0632; Tu, Qichao; Wang, Aijie; Zhang, Tong; He, Zhili; Keller, Jurg; Nielsen, Per H., 0000-0002-6402-1877; Alvarez, Pedro J. J.; Criddle, Craig S.; Wagner, Michael, 0000-0002-9778-7684; Tiedje, James M.; He, Qiang, 0000-0002-7155-6474; Curtis, Thomas P.; Stahl, David A.; Alvarez-Cohen, Lisa; Rittmann, Bruce E.; Wen, Xianghua, 0000-0002-9792-8678; Zhou, Jizhong, 0000-0003-2014-0564 Nature Microbiology 2019
25212 10.1038/s41579-018-0136-7 An Evolving View Of Methane Metabolism In The Archaea Evans, Paul N.; Boyd, Joel A.; Leu, Andy O.; Woodcroft, Ben J.; Parks, Donovan H., 0000-0001-6662-9010; Hugenholtz, Philip; Tyson, Gene W., 0000-0001-8559-9427 Nature Reviews Microbiology 2019
25221 10.1038/s41579-019-0191-8 The Ancestral And Industrialized Gut Microbiota And Implications For Human Health Sonnenburg, Erica D.; Sonnenburg, Justin L., 0000-0003-2299-6817 Nature Reviews Microbiology 2019
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25571 10.1038/s41586-018-0617-x Temporal Development Of The Gut Microbiome In Early Childhood From The Teddy Study Stewart, Christopher J.; Ajami, Nadim J.; O’Brien, Jacqueline L.; Hutchinson, Diane S.; Smith, Daniel P.; Wong, Matthew C.; Ross, Matthew C.; Lloyd, Richard E.; Doddapaneni, Harshavardhan; Metcalf, Ginger A.; Muzny, Donna; Gibbs, Richard A.; Vatanen, Tommi; Huttenhower, Curtis; Xavier, Ramnik J.; Rewers, Marian; Hagopian, William; Toppari, Jorma; Ziegler, Anette-G.; She, Jin-Xiong; Akolkar, Beena; Lernmark, Ake; Hyoty, Heikki; Vehik, Kendra; Krischer, Jeffrey P.; Petrosino, Joseph F. Nature 2018
25573 10.1038/s41586-018-0620-2 The Human Gut Microbiome In Early-Onset Type 1 Diabetes From The Teddy Study Vatanen, Tommi; Franzosa, Eric A.; Schwager, Randall; Tripathi, Surya; Arthur, Timothy D.; Vehik, Kendra; Lernmark, Ake; Hagopian, William A.; Rewers, Marian J.; She, Jin-Xiong; Toppari, Jorma; Ziegler, Anette-G.; Akolkar, Beena; Krischer, Jeffrey P.; Stewart, Christopher J.; Ajami, Nadim J.; Petrosino, Joseph F.; Gevers, Dirk; Lahdesmaki, Harri; Vlamakis, Hera; Huttenhower, Curtis; Xavier, Ramnik J. Nature 2018
25680 10.1038/s41586-019-0965-1 A New Genomic Blueprint Of The Human Gut Microbiota Almeida, Alexandre; Mitchell, Alex L.; Boland, Miguel; Forster, Samuel C.; Gloor, Gregory B.; Tarkowska, Aleksandra; Lawley, Trevor D.; Finn, Robert D. Nature 2019
25722 10.1038/s41586-019-1058-x New Insights From Uncultivated Genomes Of The Global Human Gut Microbiome Nayfach, Stephen; Shi, Zhou Jason; Seshadri, Rekha; Pollard, Katherine S.; Kyrpides, Nikos C. Nature 2019
25725 10.1038/s41586-019-1065-y Structural Variation In The Gut Microbiome Associates With Host Health Zeevi, David; Korem, Tal; Godneva, Anastasia; Bar, Noam; Kurilshikov, Alexander; Lotan-Pompan, Maya; Weinberger, Adina; Fu, Jingyuan; Wijmenga, Cisca; Zhernakova, Alexandra; Segal, Eran Nature 2019
25847 10.1038/s41586-019-1451-5 Human Placenta Has No Microbiome But Can Contain Potential Pathogens De Goffau, Marcus C.; Lager, Susanne; Sovio, Ulla; Gaccioli, Francesca; Cook, Emma; Peacock, Sharon J.; Parkhill, Julian; Charnock-Jones, D. Stephen; Smith, Gordon C. S. Nature 2019
25873 10.1038/s41586-019-1560-1 Stunted Microbiota And Opportunistic Pathogen Colonization In Caesarean-Section Birth Shao, Yan; Forster, Samuel C.; Tsaliki, Evdokia; Vervier, Kevin; Strang, Angela; Simpson, Nandi; Kumar, Nitin; Stares, Mark D.; Rodger, Alison; Brocklehurst, Peter; Field, Nigel; Lawley, Trevor D. Nature 2019
25971 10.1038/s41586-019-1916-6 Isolation Of An Archaeon At The Prokaryote<U+2013>Eukaryote Interface Imachi, Hiroyuki; Nobu, Masaru K.; Nakahara, Nozomi; Morono, Yuki; Ogawara, Miyuki; Takaki, Yoshihiro; Takano, Yoshinori; Uematsu, Katsuyuki; Ikuta, Tetsuro; Ito, Motoo; Matsui, Yohei; Miyazaki, Masayuki; Murata, Kazuyoshi; Saito, Yumi; Sakai, Sanae; Song, Chihong; Tasumi, Eiji; Yamanaka, Yuko; Yamaguchi, Takashi; Kamagata, Yoichi; Tamaki, Hideyuki; Takai, Ken Nature 2020
26179 10.1038/s41587-018-0008-8 1,520 Reference Genomes From Cultivated Human Gut Bacteria Enable Functional Microbiome Analyses Zou, Yuanqiang, 0000-0003-2380-264X; Xue, Wenbin; Luo, Guangwen; Deng, Ziqing, 0000-0001-8726-0160; Qin, Panpan, 0000-0002-7307-8736; Guo, Ruijin; Sun, Haipeng; Xia, Yan; Liang, Suisha; Dai, Ying; Wan, Daiwei; Jiang, Rongrong; Su, Lili; Feng, Qiang; Jie, Zhuye; Guo, Tongkun; Xia, Zhongkui; Liu, Chuan; Yu, Jinghong; Lin, Yuxiang; Tang, Shanmei; Huo, Guicheng; Xu, Xun; Hou, Yong, 0000-0002-0420-0726; Liu, Xin, 0000-0003-3256-2940; Wang, Jian; Yang, Huanming; Kristiansen, Karsten, 0000-0002-6024-0917; Li, Junhua, 0000-0001-6784-1873; Jia, Huijue, 0000-0002-3592-126X; Xiao, Liang, 0000-0003-0836-4397 Nature Biotechnology 2019
26180 10.1038/s41587-018-0009-7 A Human Gut Bacterial Genome And Culture Collection For Improved Metagenomic Analyses Forster, Samuel C., 0000-0003-4144-2537; Kumar, Nitin; Anonye, Blessing O., 0000-0003-1619-5554; Almeida, Alexandre, 0000-0001-8803-0893; Viciani, Elisa; Stares, Mark D.; Dunn, Matthew; Mkandawire, Tapoka T.; Zhu, Ana; Shao, Yan, 0000-0002-8662-0504; Pike, Lindsay J.; Louie, Thomas; Browne, Hilary P., 0000-0002-1305-2470; Mitchell, Alex L.; Neville, B. Anne; Finn, Robert D., 0000-0001-8626-2148; Lawley, Trevor D. Nature Biotechnology 2019
26220 10.1038/s41587-019-0191-2 Hybrid Metagenomic Assembly Enables High-Resolution Analysis Of Resistance Determinants And Mobile Elements In Human Microbiomes Bertrand, Denis; Shaw, Jim; Kalathiyappan, Manesh; Ng, Amanda Hui Qi; Kumar, M. Senthil; Li, Chenhao, 0000-0003-1182-6804; Dvornicic, Mirta; Soldo, Janja Paliska; Koh, Jia Yu; Tong, Chengxuan; Ng, Oon Tek; Barkham, Timothy, 0000-0003-0975-2244; Young, Barnaby; Marimuthu, Kalisvar; Chng, Kern Rei; Sikic, Mile, 0000-0002-8370-0891; Nagarajan, Niranjan, 0000-0003-0850-5604 Nature Biotechnology 2019
26225 10.1038/s41587-019-0202-3 Compendium Of 4,941 Rumen Metagenome-Assembled Genomes For Rumen Microbiome Biology And Enzyme Discovery Stewart, Robert D.; Auffret, Marc D., 0000-0002-2321-8219; Warr, Amanda; Walker, Alan W., 0000-0001-5099-8495; Roehe, Rainer, 0000-0002-4880-3756; Watson, Mick, 0000-0003-4211-0358 Nature Biotechnology 2019
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26265 10.1038/s41587-020-0422-6 Complete, Closed Bacterial Genomes From Microbiomes Using Nanopore Sequencing Moss, Eli L.; Maghini, Dylan G.; Bhatt, Ami S., 0000-0001-8099-2975 Nature Biotechnology 2020
26281 10.1038/s41587-020-0501-8 A Complete Domain-To-Species Taxonomy For Bacteria And Archaea Parks, Donovan H., 0000-0001-6662-9010; Chuvochina, Maria; Chaumeil, Pierre-Alain; Rinke, Christian, 0000-0003-4632-1187; Mussig, Aaron J., 0000-0002-9988-0866; Hugenholtz, Philip, 0000-0001-5386-7925 Nature Biotechnology 2020
26288 10.1038/s41587-020-0548-6 Picrust2 For Prediction Of Metagenome Functions Douglas, Gavin M.; Maffei, Vincent J., 0000-0002-5339-5945; Zaneveld, Jesse R.; Yurgel, Svetlana N.; Brown, James R., 0000-0002-9368-627X; Taylor, Christopher M., 0000-0002-7983-5275; Huttenhower, Curtis, 0000-0002-1110-0096; Langille, Morgan G. I., 0000-0002-6604-3009 Nature Biotechnology 2020
26293 10.1038/s41587-020-0603-3 A Unified Catalog Of 204,938 Reference Genomes From The Human Gut Microbiome Almeida, Alexandre, 0000-0001-8803-0893; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco, 0000-0002-6845-6982; Beracochea, Martin, 0000-0003-3472-3736; Shi, Zhou Jason; Pollard, Katherine S., 0000-0002-9870-6196; Sakharova, Ekaterina; Parks, Donovan H., 0000-0001-6662-9010; Hugenholtz, Philip, 0000-0001-5386-7925; Segata, Nicola, 0000-0002-1583-5794; Kyrpides, Nikos C., 0000-0002-6131-0462; Finn, Robert D., 0000-0001-8626-2148 Nature Biotechnology 2020
26300 10.1038/s41587-020-0718-6 A Genomic Catalog Of Earth’S Microbiomes Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel, 0000-0002-3491-0198; Varghese, Neha; Schulz, Frederik, 0000-0002-4932-4677; Wu, Dongying; Paez-Espino, David, 0000-0002-2939-5398; Chen, I-Min, 0000-0003-2026-9798; Huntemann, Marcel, 0000-0002-1284-3748; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim, 0000-0002-6322-2271; Reddy, T. B. 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26564 10.1038/s41591-018-0160-1 Depicting The Composition Of Gut Microbiota In A Population With Varied Ethnic Origins But Shared Geography Deschasaux, Melanie, 0000-0002-3359-420X; Bouter, Kristien E.; Prodan, Andrei; Levin, Evgeni; Groen, Albert K.; Herrema, Hilde; Tremaroli, Valentina; Bakker, Guido J.; Attaye, Ilias; Pinto-Sietsma, Sara-Joan; Van Raalte, Daniel H.; Snijder, Marieke B.; Nicolaou, Mary; Peters, Ron; Zwinderman, Aeilko H.; Backhed, Fredrik; Nieuwdorp, Max Nature Medicine 2018
26565 10.1038/s41591-018-0164-x Regional Variation Limits Applications Of Healthy Gut Microbiome Reference Ranges And Disease Models He, Yan; Wu, Wei; Zheng, Hui-Min; Li, Pan; Mcdonald, Daniel; Sheng, Hua-Fang; Chen, Mu-Xuan; Chen, Zi-Hui; Ji, Gui-Yuan; Zheng, Zhong-Dai-Xi; Mujagond, Prabhakar; Chen, Xiao-Jiao; Rong, Zu-Hua; Chen, Peng; Lyu, Li-Yi; Wang, Xian; Wu, Chong-Bin; Yu, Nan; Xu, Yan-Jun; Yin, Jia; Raes, Jeroen; Knight, Rob, 0000-0002-0975-9019; Ma, Wen-Jun; Zhou, Hong-Wei, 0000-0003-2472-8541 Nature Medicine 2018
26683 10.1038/s41591-019-0559-3 A Library Of Human Gut Bacterial Isolates Paired With Longitudinal Multiomics Data Enables Mechanistic Microbiome Research Poyet, M.; Groussin, M.; Gibbons, S. M., 0000-0002-8724-7916; Avila-Pacheco, J.; Jiang, X.; Kearney, S. M.; Perrotta, A. R.; Berdy, B., 0000-0002-8593-0762; Zhao, S.; Lieberman, T. D.; Swanson, P. K.; Smith, M.; Roesemann, S., 0000-0002-9466-0733; Alexander, J. E.; Rich, S. A.; Livny, J.; Vlamakis, H.; Clish, C., 0000-0001-8259-9245; Bullock, K.; Deik, A.; Scott, J.; Pierce, K. A.; Xavier, R. J.; Alm, E. J., 0000-0001-8294-9364 Nature Medicine 2019
26721 10.1038/s41591-020-0761-3 Viable Bacterial Colonization Is Highly Limited In The Human Intestine In Utero Rackaityte, E., 0000-0003-3889-8082; Halkias, J., 0000-0003-0721-8961; Fukui, E. M.; Mendoza, V. F.; Hayzelden, C.; Crawford, E. D., 0000-0003-4182-2337; Fujimura, K. E.; Burt, T. D., 0000-0001-7933-529X; Lynch, S. V., 0000-0001-5695-7336 Nature Medicine 2020
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30874 10.1093/femsec/fiz045 Issues And Current Standards Of Controls In Microbiome Research Hornung, Bastian V H; Zwittink, Romy D; Kuijper, Ed J Fems Microbiology Ecology 2019
30902 10.1093/gigascience/giz043 Ultra-Deep, Long-Read Nanopore Sequencing Of Mock Microbial Community Standards Nicholls, Samuel M, 0000-0003-4081-065X; Quick, Joshua C, 0000-0001-6376-871X; Tang, Shuiquan; Loman, Nicholas J, 0000-0002-9843-8988 Gigascience 2019
31237 10.1093/nar/gkz246 Annotree: Visualization And Exploration Of A Functionally Annotated Microbial Tree Of Life Mendler, Kerrin; Chen, Han; Parks, Donovan H; Lobb, Briallen; Hug, Laura A; Doxey, Andrew C Nucleic Acids Research 2019
31376 10.1093/sysbio/syy054 Epa-Ng: Massively Parallel Evolutionary Placement Of Genetic Sequences Barbera, Pierre; Kozlov, Alexey M; Czech, Lucas; Morel, Benoit; Darriba, Diego; Flouri, Toma<U+0161>; Stamatakis, Alexandros Systematic Biology 2018
31652 10.1101/gr.258640.119 Accurate And Complete Genomes From Metagenomes Chen, Lin-Xing, 0000-0003-2774-1952; Anantharaman, Karthik, 0000-0002-9584-2491; Shaiber, Alon, 0000-0002-4806-9280; Eren, A. Murat, 0000-0001-9013-4827; Banfield, Jillian F., 0000-0001-8203-8771 Genome Research 2020
32734 10.1111/1755-0998.13011 Laboratory Contamination Over Time During Low‐Biomass Sample Analysis Weyrich, Laura S., 0000-0001-5243-4634; Farrer, Andrew G.; Eisenhofer, Raphael; Arriola, Luis A.; Young, Jennifer; Selway, Caitlin A.; Handsley‐Davis, Matilda; Adler, Christina J.; Breen, James; Cooper, Alan Molecular Ecology Resources 2019
33474 10.1126/sciadv.aau9124 Antibiotic Resistance In European Wastewater Treatment Plants Mirrors The Pattern Of Clinical Antibiotic Resistance Prevalence Parnanen, Katariina M. M., 0000-0003-2220-1738; Narciso-Da-Rocha, Carlos, 0000-0001-6398-1633; Kneis, David, 0000-0002-6048-6984; Berendonk, Thomas U., 0000-0002-9301-1803; Cacace, Damiano, 0000-0003-1725-1044; Do, Thi Thuy; Elpers, Christian; Fatta-Kassinos, Despo; Henriques, Isabel; Jaeger, Thomas; Karkman, Antti, 0000-0003-0983-3319; Martinez, Jose Luis; Michael, Stella G.; Michael-Kordatou, Irene; O’Sullivan, Kristin; Rodriguez-Mozaz, Sara, 0000-0003-2962-8144; Schwartz, Thomas; Sheng, Hongjie; Sorum, Henning, 0000-0002-2834-3342; Stedtfeld, Robert D., 0000-0003-2678-7801; Tiedje, James M., 0000-0002-8992-6218; Giustina, Saulo Varela Della; Walsh, Fiona; Vaz-Moreira, Ivone; Virta, Marko, 0000-0001-5981-7566; Manaia, Celia M., 0000-0002-3674-1789 Science Advances 2019
34153 10.1128/cmr.00088-17 Mobile Genetic Elements Associated With Antimicrobial Resistance Partridge, Sally R.; Kwong, Stephen M.; Firth, Neville; Jensen, Slade O. Clinical Microbiology Reviews 2018
34242 10.1128/msystems.00016-19 A Novel Sparse Compositional Technique Reveals Microbial Perturbations Martino, Cameron; Morton, James T.; Marotz, Clarisse A.; Thompson, Luke R., 0000-0002-3911-1280; Tripathi, Anupriya; Knight, Rob; Zengler, Karsten Msystems 2019
34243 10.1128/msystems.00031-18 American Gut: An Open Platform For Citizen Science Microbiome Research Mcdonald, Daniel, 0000-0003-0876-9060; Hyde, Embriette; Debelius, Justine W.; Morton, James T.; Gonzalez, Antonio; Ackermann, Gail; Aksenov, Alexander A.; Behsaz, Bahar; Brennan, Caitriona; Chen, Yingfeng; Deright Goldasich, Lindsay; Dorrestein, Pieter C.; Dunn, Robert R.; Fahimipour, Ashkaan K.; Gaffney, James; Gilbert, Jack A.; Gogul, Grant; Green, Jessica L.; Hugenholtz, Philip; Humphrey, Greg; Huttenhower, Curtis; Jackson, Matthew A.; Janssen, Stefan, 0000-0003-0955-0589; Jeste, Dilip V.; Jiang, Lingjing; Kelley, Scott T., 0000-0001-9547-4169; Knights, Dan; Kosciolek, Tomasz; Ladau, Joshua; Leach, Jeff; Marotz, Clarisse; Meleshko, Dmitry; Melnik, Alexey V.; Metcalf, Jessica L.; Mohimani, Hosein; Montassier, Emmanuel, 0000-0002-2313-1172; Navas-Molina, Jose; Nguyen, Tanya T.; Peddada, Shyamal; Pevzner, Pavel; Pollard, Katherine S.; Rahnavard, Gholamali, 0000-0002-9710-0248; Robbins-Pianka, Adam; Sangwan, Naseer; Shorenstein, Joshua; Smarr, Larry; Song, Se Jin, 0000-0003-0750-5709; Spector, Timothy; Swafford, Austin D.; Thackray, Varykina G.; Thompson, Luke R.; Tripathi, Anupriya; Vazquez-Baeza, Yoshiki; Vrbanac, Alison; Wischmeyer, Paul; Wolfe, Elaine; Zhu, Qiyun; Knight, Rob Msystems 2018
34245 10.1128/msystems.00069-18 Evaluating The Information Content Of Shallow Shotgun Metagenomics Hillmann, Benjamin; Al-Ghalith, Gabriel A., 0000-0002-6953-6319; Shields-Cutler, Robin R.; Zhu, Qiyun; Gohl, Daryl M.; Beckman, Kenneth B.; Knight, Rob; Knights, Dan Msystems 2018
34247 10.1128/msystems.00186-19 Quantifying And Understanding Well-To-Well Contamination In Microbiome Research Minich, Jeremiah J.; Sanders, Jon G.; Amir, Amnon; Humphrey, Greg; Gilbert, Jack A.; Knight, Rob Msystems 2019
34254 10.1128/msystems.00290-19 Controlling For Contaminants In Low-Biomass 16S Rrna Gene Sequencing Experiments Karstens, Lisa; Asquith, Mark; Davin, Sean; Fair, Damien; Gregory, W. Thomas; Wolfe, Alan J.; Braun, Jonathan; Mcweeney, Shannon Msystems 2019
34266 10.1136/annrheumdis-2018-214514 Prevotella Copri In Individuals At Risk For Rheumatoid Arthritis Alpizar-Rodriguez, Deshire, 0000-0002-6930-0517; Lesker, Till Robin; Gronow, Achim; Gilbert, Benoit; Raemy, Elena; Lamacchia, Celine; Gabay, Cem; Finckh, Axel; Strowig, Till Annals Of The Rheumatic Diseases 2019
34481 10.1136/gutjnl-2019-319654 Mediterranean Diet Intervention Alters The Gut Microbiome In Older People Reducing Frailty And Improving Health Status: The Nu-Age 1-Year Dietary Intervention Across Five European Countries Ghosh, Tarini Shankar; Rampelli, Simone; Jeffery, Ian B; Santoro, Aurelia; Neto, Marta; Capri, Miriam; Giampieri, Enrico; Jennings, Amy, 0000-0001-5333-714X; Candela, Marco; Turroni, Silvia; Zoetendal, Erwin G; Hermes, Gerben D A, 0000-0003-4314-9553; Elodie, Caumon; Meunier, Nathalie; Brugere, Corinne Malpuech; Pujos-Guillot, Estelle; Berendsen, Agnes M; De Groot, Lisette C P G M; Feskins, Edith J M; Kaluza, Joanna, 0000-0001-9454-0929; Pietruszka, Barbara, 0000-0003-0731-8612; Bielak, Marta Jeruszka; Comte, Blandine; Maijo-Ferre, Monica; Nicoletti, Claudio; De Vos, Willem M; Fairweather-Tait, Susan; Cassidy, Aedin; Brigidi, Patrizia; Franceschi, Claudio; O’Toole, Paul W, 0000-0001-5377-0824 Gut 2020
34484 10.1136/gutjnl-2019-320438 Mediterranean Diet Intervention In Overweight And Obese Subjects Lowers Plasma Cholesterol And Causes Changes In The Gut Microbiome And Metabolome Independently Of Energy Intake Meslier, Victoria; Laiola, Manolo; Roager, Henrik Munch, 0000-0002-2504-8313; De Filippis, Francesca; Roume, Hugo; Quinquis, Benoit; Giacco, Rosalba; Mennella, Ilario; Ferracane, Rosalia; Pons, Nicolas; Pasolli, Edoardo; Rivellese, Angela; Dragsted, Lars Ove, 0000-0003-0609-6317; Vitaglione, Paola; Ehrlich, Stanislav Dusko, 0000-0002-7563-4046; Ercolini, Danilo, 0000-0003-3061-9560 Gut 2020
36501 10.1186/s40168-018-0470-z Optimizing Taxonomic Classification Of Marker-Gene Amplicon Sequences With Qiime 2’S Q2-Feature-Classifier Plugin Bokulich, Nicholas A.; Kaehler, Benjamin D.; Rideout, Jai Ram; Dillon, Matthew; Bolyen, Evan; Knight, Rob; Huttley, Gavin A.; Gregory Caporaso, J. Microbiome 2018
36502 10.1186/s40168-018-0541-1 Metawrap―A Flexible Pipeline For Genome-Resolved Metagenomic Data Analysis Uritskiy, Gherman V.; Diruggiero, Jocelyne, 0000-0001-6721-8061; Taylor, James Microbiome 2018
36503 10.1186/s40168-018-0575-4 Lack Of Detection Of A Human Placenta Microbiome In Samples From Preterm And Term Deliveries Leiby, Jacob S.; Mccormick, Kevin; Sherrill-Mix, Scott; Clarke, Erik L.; Kessler, Lyanna R.; Taylor, Louis J.; Hofstaedter, Casey E.; Roche, Aoife M.; Mattei, Lisa M.; Bittinger, Kyle; Elovitz, Michal A.; Leite, Rita; Parry, Samuel; Bushman, Frederic D., 0000-0003-4740-4056 Microbiome 2018
36506 10.1186/s40168-018-0605-2 Simple Statistical Identification And Removal Of Contaminant Sequences In Marker-Gene And Metagenomics Data Davis, Nicole M.; Proctor, Diana M.; Holmes, Susan P.; Relman, David A.; Callahan, Benjamin J., 0000-0002-8752-117X Microbiome 2018
36512 10.1186/s40168-019-0663-0 Mobile Antibiotic Resistome In Wastewater Treatment Plants Revealed By Nanopore Metagenomic Sequencing Che, You; Xia, Yu; Liu, Lei; Li, An-Dong; Yang, Yu; Zhang, Tong, 0000-0003-1148-4322 Microbiome 2019
37098 10.1371/journal.pbio.2006842 Gut Microbiota Diversity Across Ethnicities In The United States Brooks, Andrew W., 0000-0002-9237-5349; Priya, Sambhawa; Blekhman, Ran; Bordenstein, Seth R. Plos Biology 2018
37103 10.1371/journal.pbio.3000102 Evolutionary Dynamics Of Bacteria In The Gut Microbiome Within And Across Hosts Garud, Nandita R., 0000-0003-4217-4407; Good, Benjamin H., 0000-0002-7757-3347; Hallatschek, Oskar, 0000-0002-1312-5975; Pollard, Katherine S., 0000-0002-9870-6196 Plos Biology 2019
38489 10.3389/fmicb.2019.01124 The Not-So-Sterile Womb: Evidence That The Human Fetus Is Exposed To Bacteria Prior To Birth Stinson, Lisa F.; Boyce, Mary C.; Payne, Matthew S.; Keelan, Jeffrey A. Frontiers In Microbiology 2019
38575 10.3389/fnut.2019.00004 Breast Milk Microbiota Is Shaped By Mode Of Delivery And Intrapartum Antibiotic Exposure Hermansson, Henriina; Kumar, Himanshu; Collado, Maria Carmen; Salminen, Seppo; Isolauri, Erika; Rautava, Samuli Frontiers In Nutrition 2019
38579 10.3389/fnut.2019.00045 What’S Normal? Microbiomes In Human Milk And Infant Feces Are Related To Each Other But Vary Geographically: The Inspire Study Lackey, Kimberly A.; Williams, Janet E.; Meehan, Courtney L.; Zachek, Jessica A.; Benda, Elizabeth D.; Price, William J.; Foster, James A.; Sellen, Daniel W.; Kamau-Mbuthia, Elizabeth W.; Kamundia, Egidioh W.; Mbugua, Samwel; Moore, Sophie E.; Prentice, Andrew M.; K., Debela Gindola; Kvist, Linda J.; Otoo, Gloria E.; Garcia-Carral, Cristina; Jimenez, Esther; Ruiz, Lorena; Rodriguez, Juan M.; Pareja, Rossina G.; Bode, Lars; Mcguire, Mark A.; Mcguire, Michelle K. Frontiers In Nutrition 2019
39640 10.3390/nu11122862 Effect Of Diet On The Gut Microbiota: Rethinking Intervention Duration Leeming, Emily R; Johnson, Abigail J, 0000-0002-5998-4724; Spector, Tim D; Le Roy, Caroline I, 0000-0002-0341-751X Nutrients 2019
39651 10.3390/nu12041039 Breast Milk, A Source Of Beneficial Microbes And Associated Benefits For Infant Health Lyons, Katriona E.; Ryan, C. Anthony; Dempsey, Eugene M.; Ross, R. Paul; Stanton, Catherine Nutrients 2020
40673 10.7717/peerj.7359 Metabat 2: An Adaptive Binning Algorithm For Robust And Efficient Genome Reconstruction From Metagenome Assemblies Kang, Dongwan D.; Li, Feng; Kirton, Edward, 0000-0003-1974-1768; Thomas, Ashleigh, 0000-0001-7422-5649; Egan, Rob, 0000-0001-7080-7801; An, Hong; Wang, Zhong, 0000-0002-6307-0458 Peerj 2019